High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Abstract

Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

Effects of Different Native Plants on Soil Remediation and Microbial Diversity in Jiulong Iron Tailings Area, Jiangxi

“…The community-level physiological profiling (CLPP) method is based on the single carbon source utilization mode of Biolog™ EcoPlate [22], which can compare different microbial communities and is suitable for comparison between contaminated and uncontaminated soil microbial communities [23,24]. With the development of molecular biology, high-throughput sequencing technology is widely regarded as an important means to evaluate the diversity and dynamics of soil microbial communities, and it has outstanding advantages over traditional culture-based methods [25]. Considering that the high-throughput method still requires a relatively high cost, its convenience and practicability in the possible large-scale tailings soil survey in the future were lower than that of using Biolog™ EcoPlate.…”

Biological Control of Plant Pathogens: A Global Perspective

“…The rhizosphere is the soil area that surrounds living roots and is influenced by plant root exudates. It is one of the most important microbial hotspots in the soil, with much greater process rates and more intensive interactions [ 22 , 23 ]. The rhizosphere contains a complex microbial community called the rhizosphere microbiome.…”

Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants

“…In alignment with this, the identification and selection of functional “culturable” organisms that integrate well with non-culturable communities have been performed at the site to be remediated. With recent advances in high-throughput molecular technologies, the development of culture-independent methods provides a platform for linking microbial community structure, interactions, and system function that may help in designing “robust” and “predictable” multispecies PGPB-based biofilms for better plant growth and soil remediation …”

“…With recent advances in high-throughput molecular technologies, the development of culture-independent methods provides a platform for linking microbial community structure, interactions, and system function that may help in designing "robust" and "predictable" multispecies PGPB-based biofilms for better plant growth and soil remediation. 70 A logical progression in the development of microbial consortia that are sympathetic to the receiving ecosystem is to become more accommodating of the microbial diversity already present at the site needing remediation. This will involve using site-specific metagenomics and other omics technologies to gain a holistic view of microbial diversity and metabolic potential in the affected environment, helping to better understand how inocula can better complement the preexisting community.…”